Difference between revisions of "HMM PD00008"

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(Created page with "Back to '''List of HMMs''' '''Symbol''': CC1_Sac_PD '''Name''': Sac phosphatase domain === Description === We built the profile because the boundary of phosphatase ...")
 
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=== Description ===
 
=== Description ===
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We built the profile because the boundary of phosphatase domain defined by Pfam profile is not the same as the one reported in crystal structure study <cite>Begley03</cite> and SMART does not have the profile for the myotubularin phosphatase domain. The crystal structure shows the phosphatase domain ranges from 205-586 in human MTMR2 (Figure 6A in <cite>Begley03</cite>). The Pfam profile [http://pfam.xfam.org/family/PF06602.10 Myotub-related (PF06602)] predicted the range from 192-529.
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Based upon the crystal structure of yeast SAC1, the yeast SAC1 has two structure domains: SacN and catalytic domain <cite>Manford10</cite> (see the sequences in supplementary materials). The SacN ranges from 1-181; the catalytic phosphatase domain ranges from 182-504.
  
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=== How the HMM was built ===
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When using the HMM/PSSM profiles of public databases to determine the region of phosphatase domain, they gave different regions from the region determined from the crystal structure paper:
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We PSI-BLASTed the region from 190 to 600 of human MTMR2. The region is the phosphatase domain determined in crystal structure study with flanking regions <cite>Begley03</cite>:
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* Pfam database: Syja_N (PF02383), 56-343
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* CDD database: 1) Cdd:pfam02383, 55-348, 2) Cdd:COG5329, 3-578
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* SMART: no hit
  
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>Hsap_MTMR2:205-586 id=HsapP048_AA CC1:CC1:Myotubularin:MTMR1 [Homo sapiens]
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In brief, Pfam profile contains part of SacN domain and part of the phosphatase domain; COG profile contains both SacN and the catalytic phosphatase domain.
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GWKLYDPLLEYRRQGIPNESWRITKINERYELCDTYPALLVVPANIPDEELKRVASFRSRGRIPVLSWIHPESQATITRCSQPMVGVSGKRSKEDEKYLQAIMDSNAQSHKIFIFDARPSVNAVANKAKGGGYESEDAYQNAELVFLDIHNIHVMRESLRKLKEIVYPNIEETHWLSNLESTHWLEHIKLILAGALRIADKVESGKTSVVVHSSDGWDRTAQLTSLAMLMLDGYYRTIRGFEVLVEKEWLSFGHRFQLRVGHGDKNHADADRSPVFLQFIDCVWQMTRQFPTAFEFNEYFLITILDHLYSCLFGTFLCNSEQQRGKENLPKRTVSLWSYINSQLEDFTNPLYGSYSNHVLYPVASMRHLELWVGYYIRWNPR
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We first PSI-BLASTed the region against RefSeq database via NCBI BLAST server. We found 5000+ hits in 1st round, which is difficult to look into. We then  PSI-BLASTed the region against RefSeq database via NCBI BLAST server. The coverage of human myotubularins:
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=== How the HMM was built ===
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* MTM1, MTMR1, MTMR2: ~190-600, 100%
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* MTMR3: ~214-595 (human, rat, mouse); MTMR4: ~225-588 (human, mouse), ~213-598 (xenopus)
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* MTMR5: ~317-535 (human), ~317-579 (mouse); MTMR13 (not in swissprot?)
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* MTMR6: ~195-595 (human, mouse); MTMR7: 192-592 (human), 203-593 (mouse); 192-593 (human, chicken)
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* MTMR9: 192-588 (human, mouse), 204-592 (cow)
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* MTMR10 (MTMRA): 214-532 (human, mouse, xenopus, zebra fish); MTMR11 (MTMRB): 214-561 (human, mouse); MTMR12 (MTMRC): 202-556 (human), 225-556 (mouse, rat, zebra fish),
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* MTMR13 (MTMRD): 223-581 (human), 345-581 (xenopus)
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The result shows we can build four individual HMMs for the subfamilies:
 
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* MTMR1, MTMR6, MTMR9 (perhaps MTMR3)
 
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* MTMR10
 
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* MTMR13
 
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* MTMR14
 
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Note: In addition to PSI-BLAST, we tried to obtain an alignment from HHPRED, but the quality is pretty bad.
 
  
 
=== References ===
 
=== References ===
 
<biblio>
 
<biblio>
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#Manford10 pmid=20389282
 
</biblio>
 
</biblio>
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=== Supplementary materials ===
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The full sequence of yeast SAC1:
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>yeast_SAC1
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MTGPIVYVQNADGIFFKLAEGKGTNDAVIHLANQDQGVRVLGAEEFPVQGEVVKIASLMGFIKLKLNRYAIIANTVEETGRFNGHVFYRVLQHSIVSTKFNSRIDSEEAEYIKLLELHLKNSTFYFSYTYDLTNSLQRNEKVGPAASWKTADERFFWNHYLTEDLRNFAHQDPRIDSFIQPVIYGYAKTVDAVLNATPIVLGLITRRSIFRAGTRYFRRGVDKDGNVGNFNETEQILLAENPESEKIHVFSFLQTRGSVPIYWAEINNLKYKPNLVLGENSLDATKKHFDQQKELYGDNYLVNLVNQKGHELPVKEGYESVVHALNDPKIHYVYFDFHHECRKMQWHRVKLLIDHLEKLGLSNEDFFHKVIDSNGNTVEIVNEQHSVVRTNCMDCLDRTNVVQSVLAQWVLQKEFESADVVATGSTWEDNAPLLTSYQNLWADNADAVSVAYSGTGALKTDFTRTGKRTRLGAFNDFLNSASRYYQNNWTDGPRQDSYDLFLGGFRPHTASIKSPFPDRRPVYIQLIPMIICAALTVLGATIFFPKDRFTSSKNLLYFAGASIVLALSTKFMFKNGIQFVNWPKLVDVGFLVVHQTHDKEQQFKGLKYAQSPKFSKPDPLKRD
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The sequence of SacN domain of SAC1:
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>yeast_SAC1_SacN
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MTGPIVYVQNADGIFFKLAEGKGTNDAVIHLANQDQGVRVLGAEEFPVQGEVVKIASLMGFIKLKLNRYAIIANTVEETGRFNGHVFYRVLQHSIVSTKFNSRIDSEEAEYIKLLELHLKNSTFYFSYTYDLTNSLQRNEKVGPAASWKTADERFFWNHYLTEDLRNFAHQDPRIDSFIQP
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The sequence of catalytic domain of yeast SAC1:
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>yeast_SAC1_Catalytic_Domain
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VIYGYAKTVDAVLNATPIVLGLITRRSIFRAGTRYFRRGVDKDGNVGNFNETEQILLAENPESEKIHVFSFLQTRGSVPIYWAEINNLKYKPNLVLGENSLDATKKHFDQQKELYGDNYLVNLVNQKGHELPVKEGYESVVHALNDPKIHYVYFDFHHECRKMQWHRVKLLIDHLEKLGLSNEDFFHKVIDSNGNTVEIVNEQHSVVRTNCMDCLDRTNVVQSVLAQWVLQKEFESADVVATGSTWEDNAPLLTSYQNLWADNADAVSVAYSGTGALKTDFTRTGKRTRLGAFNDFLNSASRYYQNNWTDGPRQDSYDLFLGG

Revision as of 19:24, 7 October 2015

Back to List of HMMs

Symbol: CC1_Sac_PD

Name: Sac phosphatase domain

Description

Based upon the crystal structure of yeast SAC1, the yeast SAC1 has two structure domains: SacN and catalytic domain [1] (see the sequences in supplementary materials). The SacN ranges from 1-181; the catalytic phosphatase domain ranges from 182-504.

When using the HMM/PSSM profiles of public databases to determine the region of phosphatase domain, they gave different regions from the region determined from the crystal structure paper:

  • Pfam database: Syja_N (PF02383), 56-343
  • CDD database: 1) Cdd:pfam02383, 55-348, 2) Cdd:COG5329, 3-578
  • SMART: no hit

In brief, Pfam profile contains part of SacN domain and part of the phosphatase domain; COG profile contains both SacN and the catalytic phosphatase domain.

How the HMM was built

References

Error fetching PMID 20389282:
  1. Error fetching PMID 20389282: [Manford10]

Supplementary materials

The full sequence of yeast SAC1:

>yeast_SAC1 MTGPIVYVQNADGIFFKLAEGKGTNDAVIHLANQDQGVRVLGAEEFPVQGEVVKIASLMGFIKLKLNRYAIIANTVEETGRFNGHVFYRVLQHSIVSTKFNSRIDSEEAEYIKLLELHLKNSTFYFSYTYDLTNSLQRNEKVGPAASWKTADERFFWNHYLTEDLRNFAHQDPRIDSFIQPVIYGYAKTVDAVLNATPIVLGLITRRSIFRAGTRYFRRGVDKDGNVGNFNETEQILLAENPESEKIHVFSFLQTRGSVPIYWAEINNLKYKPNLVLGENSLDATKKHFDQQKELYGDNYLVNLVNQKGHELPVKEGYESVVHALNDPKIHYVYFDFHHECRKMQWHRVKLLIDHLEKLGLSNEDFFHKVIDSNGNTVEIVNEQHSVVRTNCMDCLDRTNVVQSVLAQWVLQKEFESADVVATGSTWEDNAPLLTSYQNLWADNADAVSVAYSGTGALKTDFTRTGKRTRLGAFNDFLNSASRYYQNNWTDGPRQDSYDLFLGGFRPHTASIKSPFPDRRPVYIQLIPMIICAALTVLGATIFFPKDRFTSSKNLLYFAGASIVLALSTKFMFKNGIQFVNWPKLVDVGFLVVHQTHDKEQQFKGLKYAQSPKFSKPDPLKRD

The sequence of SacN domain of SAC1: >yeast_SAC1_SacN MTGPIVYVQNADGIFFKLAEGKGTNDAVIHLANQDQGVRVLGAEEFPVQGEVVKIASLMGFIKLKLNRYAIIANTVEETGRFNGHVFYRVLQHSIVSTKFNSRIDSEEAEYIKLLELHLKNSTFYFSYTYDLTNSLQRNEKVGPAASWKTADERFFWNHYLTEDLRNFAHQDPRIDSFIQP

The sequence of catalytic domain of yeast SAC1: >yeast_SAC1_Catalytic_Domain VIYGYAKTVDAVLNATPIVLGLITRRSIFRAGTRYFRRGVDKDGNVGNFNETEQILLAENPESEKIHVFSFLQTRGSVPIYWAEINNLKYKPNLVLGENSLDATKKHFDQQKELYGDNYLVNLVNQKGHELPVKEGYESVVHALNDPKIHYVYFDFHHECRKMQWHRVKLLIDHLEKLGLSNEDFFHKVIDSNGNTVEIVNEQHSVVRTNCMDCLDRTNVVQSVLAQWVLQKEFESADVVATGSTWEDNAPLLTSYQNLWADNADAVSVAYSGTGALKTDFTRTGKRTRLGAFNDFLNSASRYYQNNWTDGPRQDSYDLFLGG

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